Gene Expression.

	Affymetrix	Agilent	Illumina	NimbleGen
Amount of total RNA requested for UHNMAC service	100 ng	2 µg	100 ng	10 µg
Amplification involved in labeling the amount of RNA listed above	Yes	Yes	Yes	No
Amplification method available? Minimum amount of total RNA required	Yes, 500 pg	No (as little as 50 ng total RNA can be used, although less reliable)	No	Yes, 100 ng*
Protocol for partially degraded samples	Yes	No	Yes	No
One- or two-colour	One	Both	One (streptavidin-Cy3 staining)	Both
Probe size	25-mer	60-mer	50-mer	60-mer
Species for which catalogue arrays are available (Custom printing is available on all platforms)	Human Mouse Yeast Rat Arabidopsis Drosophila C. elegans Zebrafish & others Affymetrix is the only platform to offer catalogue Grape, Soybean & Citrus arrays	Human Mouse Yeast Rat Arabidopsis Drosophila C. elegans Zebrafish & others Agilent is the only platform to offer catalogue Brassica, Salmon & Tobacco arrays	Human Mouse Yeast	Human Mouse Yeast Rat Arabidopsis Drosophila C. elegans Zebrafish & others Prokaryotic designs covering over 200 organisms
Number of probes	Millions of features (i.e. >5.3 million on Human Exon 1.0ST array	15K, 44K, 2x105K, 244K formats available	up to 48K (Human whole genome array)	385K, HD2 (2.1 million) 4x72K 12x135K
Software for analysis	Expression Console	GeneSpring	BeadStudio	ArrayStar

* NimbleGen suggests using MessageAmp II aRNA Amplification kit (Ambion)

ChIP-on-Chip.

	Affymetrix	Agilent	NimbleGen
Amount of DNA requested for UHNMAC service	9 µg	4 µg PCR amplified	2.5 µg (385K array) 6.5 µg (HD2 array)
Probe size	25-mer	60-mer	50-75-mer
Species for which catalogue arrays are available (Custom printing is available on all platforms)	Human Mouse Yeast Arabidopsis Drosophila C. elegans Promoter-specific Chromosome 21/22 ENCODE	Human Mouse Yeast Arabidopsis Drosophila C. elegans CpG Promoter-specific ENCODE	Human Mouse Rat Drosophila C. elegans
Array formats	>6 million features possible	2x244K Custom arrays (15K, 105K, 244K)	HD2, 385K

DNA Methylation

	Agilent	Illumina	NimbleGen
Amount of DNA requested for UHNMAC service	2 µg PCR amplified or genomic	1 µg genomic DNA	1 µg PCR amplified or genomic
Probe size	60-mer	50-mer	50-75-mer
Species for which catalogue arrays are available (Custom printing is available on all platforms)	Human Mouse	Human	Human Mouse Rat Arabidopsis Dog Chicken
Array formats	2x244K Custom arrays (15K, 105K, 244K)	Human CGI 8.1K, 12K	385K, HD2

miRNA Profiling.

	Affymetrix	Agilent	Illumina
Amount of RNA requested for UHNMAC service	please inquire	100 ng total RNA	100-200 ng total RNA (DASL assay*)
One- or two-colour	One	One	One
Probe size	25-mer	60-mer	50-mer
Species for which arrays are available	Human Mouse Rat Canine Monkey *all species represented on one array*	Human Mouse Rat Custom printing available	Human Mouse Custom printing available
Sanger miRNA database version number used (as of March 9, 2009)	ver.11	Human:ver.12 Mouse: ver.12 Rat: ver.10.1 Custom	ver.12
Array formats	mini-array (format 400) 4 identical sense probes for each miRNA	8x15K Human: 866 + 89 human viral Mouse: 627 + 39 mouse viral Rat: 350	12 sample BeadChip Human: 1146 Mouse: 656

* DASL assay: cDNA-mediated Annealing, Selection, extension, Ligation assay

Array CGH.*

	Agilent	NimbleGen
Amount of genomic DNA requested for service	3 µg	1-5 µg
Amount of DNA required for amplification method, if available	100 ng	N/A
Probe size	60-mer	50-75-mer
Species for which catalogue arrays are available (Custom printing is available on both platforms)	Human Mouse Rat	Human Mouse Rat Drosophila C. elegans S. cerevisiae S. pombe Zebrafish Chicken Cow P. falciparum 3D7
Array formats	244K, 2x105K, 4x44K	Human: 2.1M, 385K, 12x135K, 4x72K; Mouse & others: mostly 385K

* cDNA arrays can also be used for aCGH, read more

cDNA Microarrays

Advantages	Disadvantages
Increased detection sensitivity due to longer sequences	Cross-hybridisation can be a problem
Affordable (production cost is lower than for oligonucleotide arrays)	Maintaining clones and PCR amplification is labour-intensive (not a problem if you are purchasing printed arrays)
Allows representation of entire genome on one array
No prior knowledge of gene sequence required (use of clone library); no probe design involved

Oligonucleotide arrays (in general)

Advantages	Disadvantages
Higher specificity (less cross-hybridisation due to shorter probes)	Decreased sensitivity due to shorter sequences (lower sensitivity compensated by use of multiple probes)
More uniform melting temperatures	Expensive to design and manufacture
Detection of SNP and splice variants	Prior knowledge of sequence required
Higher uniformity of spots (controlled amount of material per spot)

Affymetrix and Agilent Oligonucleotide arrays

Affymetrix	Agilent
Only 1-colour is offered	Offers both 1- and 2-colour systems
Decreased sensitivity due to shorter sequences (25-mer); however, lower sensitivity compensated by the fact that multiple oligos represent each gene	Longer 60-mers are more tolerant of sequence mismatches and thus are more suitable for analysis of highly polymorphic regions
RNA amplification is part of RNA labeling protocol; can be fairly expensive (compared with cDNA arrays)	RNA amplification is part of RNA labeling protocol; can be fairly expensive (compared with cDNA arrays)
Additional equipment (specialised fluidics station and Affymetrix-specific scanner) required

Agilent 1-colour versus 2-colour

• 1-colour allows for experimental design to change throughout project - good for projects that will take place over a long period of time with an unknown number of samples
• 2-colour is a more direct comparison of two samples

Table 1. The strengths and weaknesses of NGS and microarrays.
(This table was taken from Asmann et al. Gastroenterology 2008, 135:1466)

Microarray Analysis		Massively parallel, or next-generation, sequencing
Pros	Cons	Pros	Cons
Relatively inexpensive	High background, low sensitivity	Low background, very sensitive	Expensive
Easy sample preparation	Limited dynamic range	Large dynamic range	Complex sample preparation
Mature informatics and statistics	Not quantitative	Quantitative	Limited bioinformatics
	Competitive hybridisation		Massive information technology infrastructure required
	Annotation of probes

Table 2. Comparison of Roche, Illumina, and Applied Biosystems NGS platforms.

	Roche (454): Titanium series reagents (run on FLX Genome Sequencer)	Illumina: Genome Analyser II	Applied Biosystems: SOLiDTM
Sequencing chemistry	pyrosequencing	polymerase-based sequencing-by-synthesis	Ligation-based sequencing
Amplification approach	Emulsion PCR	Bridge amplification	Emulsion PCR
MB/run	400-600 MB	1300 MB	3000 MB
Time/run	10 hr	4 days	5 days
Read length	400 bp	up to 75 bp	35 bp